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The film is set during the transition period between the Sui Dynasty and the Tang Dynasty. It opens with various shots of the Shaolin Temple, including the wall paintings, the many beautiful trees, gardens, shrines, gates, and statues of Buddha and the Gods. The temple bells toll as the monks kneel in the pillared inner sanctum and bow before the great altar of the Golden Buddha, before which sits the Abbot of Shaolin. A shaven-headed, blue-robed novice (Jet Li) stands with his palms pressed together and his head bowed. He is about to be accepted into the Shaolin Temple. The Abbot speaks to him of ceremony, purification, and learning to respect one's self and others. Then the Abbot asks for his name. "Jue Yuan", he answers. The Abbot tells him that to be accepted into the Shaolin Temple, he must vow to not commit murder. He asks if he can obey this, but Jue Yuan is silent, staring downward. The Abbot repeats the question, and Jue Yuan slowly raises his eyes, gazing intensely at him. The Abbot asks the question a third time...

The film flashes back to the warlord and deadly fighter Wang Shichong killing an old man with a throat lock and throwing him off a high brick wall into a muddy river, then abusively ordering the rest of his slaves back to work. They're at a labor camp by the great river, toiling in the mud among corpses that hang from gallows as the soldiers whip them. It is during the rebellions at the end of the Sui Dynasty, when China became divided between various factions. Wang Shichong, who ruled from Luoyang, has treacherously installed himself as Emperor of the East Capitol, and is overseeing the bolstering of his riverfront defenses against the rival warlords on the opposite bank. They are near the Shaolin Temple. He forces even the old, crippled, and sick to work, but still the work isn't progressing fast enough for him. He orders an officer to bring all his prisoners, who are opposing rebels, to join the slaves.

These rebels include an older kung fu master, famous for his kicking skill, and his long-haired son, Jue Yuan. The soldiers whip the slaves, and one old slave collapses and drops a wooden beam, which causes an officer's horse to rear and throw the officer. The officer begins to beat the slave to death, but Jue Yuan's father attacks him, though his ankles and wrists are chained together. The officer proves to be a kung fu fighter, and they fight, but Jue Yuan's father still manages to defeat him. This draws the attention of the Emperor, who attacks Jue Yuan's father himself and rips his throat out with his bare hand. Jue Yuan rushes in and unleashes the kicking skills that his father taught him, scattering the guards and fighting the officers, but then the Emperor beats him up and deals him a deadly Dim Mak palm strike to the chest. Jue Yuan is thrown into the river, and he manages to swim away and escape. He staggers through the wild, dying of his wounds, but finally he manages to reach the Shaolin Temple. The Sifu (Yu Hai) is teaching the monks staff kung fu when Jue Yuan arrives and falls unconscious.

Throngs of refugees from the war-torn countryside are flocking to the Shaolin Temple every day. The Abbot proclaims that it is their holy duty as Buddhist monks to pray for the refugees and do all they can to help them. They nurse Jue Yuan back to health. When he has recovered, he joins them in carrying water from the river to the Temple, which they use as kung fu conditioning. He struggles, but is helped by a beautiful girl named Bai Wu Xia (Ding Lan), who sings and herds rams in the beautiful wildlife-filled forested hills that surround the Shaolin Temple.

Jue Yuan spies on the monks' kung fu training and gets himself into various other comedic misadventures around the Shaolin Temple, befriending the light-hearted, fun-loving, mischievous Sifu and his equally mischievous kung fu students in the process. One night they all sneak out to eat and party around a fire in the woods. There he learns more about the Sifu and his former family in the North.

He learns that the Sifu is Bai Wu Xia's father, that she was one of the main ones who nursed him back to health, and that she is skilled at kung fu. The Sifu says that nine years ago, he and his wife were being chased by the Emperor and his soldiers, and he left his wife with a farmer to hide while he fled on, eventually hiding in the Shaolin Temple. The farmer, who had no children, spoiled Bai Wu Xia when she was young.

Jue Yuan declares that he will kill the Emperor, and he asks the Sifu to train him in his Northern Shaolin kung fu. The Sifu tells him that Shaolin kung fu is for defense, not killing, and besides, Jue Yuan isn't a monk. Jue Yuan drops to his knees, presses his palms together, and says that he wants to become a monk.

Jue Yuan’s head is shaven, and he bows before the Abbot of Shaolin on the great altar of the golden Buddha. The assembled monks sing mystic hymns, ring bells, and strike gongs. A mosquito bites Jue Yuan as he kneels there, and he kills it, but the Abbot blesses and accepts him, and he is ordained as a junior monk.

Jue Yuan joins his fellow monks in Northern Shaolin kung fu training. After a time of at least several months he has gained impressive fighting abilities, but while sparring, his enemy flashes with the visage of the Emperor in his mind, and he almost kills his partner. He is banned from practicing kung fu. His emotions flare quickly out of control, and he runs away from the Shaolin Temple.

Jue Yuan attempts to assassinate the Emperor, but fails and is forced to flee. Ashamed, he returns to the Shaolin Temple. His Sifu admonishes him, but welcomes him home and allows him to resume his Northern Shaolin kung fu training. Jue Yuan trains for at least another year, as seen in a ‘four seasons’ training sequence, and becomes highly adept at Northern Shaolin kung fu.

Then another refugee comes fleeing to Shaolin, this one pursued by the Emperor and his men. This refugee is Li Shimin, son of a great leader who founded the Tang Dynasty, Li Yuan.

The Shaolin monks keep peace with the Emperor and his men, and make a show of helping them hunt for Li Shimin. But Jue Yuan helps Li Shimin escape through the mountains, and Jue Yuan and Li Shimin end up hiding together in an abandoned ancient mountainous cave temple with many giant statues of Buddha and the Gods. Bai Wu Xia stealthily brings them food and water.

Li Shimin must escape, though, so Jue Yuan and Bai Wu Xia help him, sneaking and bribing their way past the Emperor’s patrols in disguise. Throughout this time, a forbidden romance builds between Jue Yuan and Bai Wu Xia. But they fail in their clean escape, and Li Shimin and Bai Wu Xia flee on a raft down a river, Li Shimin with an arrow in his leg, while Jue Yuan sacrifices himself to slow down the Emperor’s outriders. However, his Sifu from Shaolin and a group of Shaolin warrior monks come to his aid and massacre the outriders. They save Jue Yuan’s life, but his Sifu excommunicates him from Shaolin for his acts and banishes him. He desperately follows them back to the Shaolin Temple anyway, but they throw him out and drive him away.

The Emperor learns what the Shaolin monks did, and marches on the Shaolin Temple with his army to destroy it.

Jue Yuan comes back yet again, and this time his Sifu sends him away along with Ba Wu Xia, to take her to safety and never return.

The Abbot of Shaolin orders the monks not to fight, even while the Emperor’s army surrounds the Shaolin Temple. The Abbot treats with the Emperor. He appeals that the Temple has a very long history, and a crime should not merit the destruction of the buildings, or any of the monks. As the Abbot, he accepts the blame. The Emperor has him placed on a great pyre, which is set aflame. He tells the monks that if they reveal the traitors’ whereabouts, he’ll spare the Temple and the Abbot’s life. When no one talks, he has his men kill several of the other top monks, and threatens that if no one talks, they’ll all be killed.

Then the Sifu and the warrior monks reveal themselves. The Sifu cries that they must fight. The Abbot, as he is immersed in fire, tells the Sifu to release the souls of the Emperor and his men and send them to Heaven. And so the battle is joined. Many monks are killed.

Jue Yuan and Ba Wu Xia return to the embattled Shaolin Temple. The Emperor’s army takes the outer walls and outer grounds, and kills all the monks therein. The surviving monks fall back within the inner walls. The Sifu is shot full of arrows. He entreats Jue Yuan to protect Shaolin and uphold justice, and dies.

The Emperor and his men break open the inner gate with a battering ram, and they’re about to massacre the rest of the monks, but then the Emperor receives word that Li Shimin and his army are approaching his own East Capital, and they abandon the siege of the Shaolin Temple and ride for the East Capital with all speed.

Jue Yuan and the warrior monks ride after the Emperor and his men and join the battle at the ravaged East Capital, at the very site where the Emperor killed Jue Yuan’s father. Jue Yuan and the Emperor duel with swords and empty hands and feet on the shores of the great river. Their battle climbs up a great wooden structure, falls off the top into the river, and returns to the shore. Finally Jue Yuan uses his Northern Shaolin kung fu to kill the Emperor, and the battle for the East Capital is won.

The film returns to its beginning, with Jue Yuan in the sanctum of the Shaolin Temple, kneeling before the high altar, as the new Abbot asks him if he can obey the vow to do no murder. Jue Yuan vows that he shall not kill save to uphold righteousness, and the Abbot accepts this. Jue Yuan continues to swear his vows, but when he reaches the vow of celibacy, he is again conflicted. He opens his folded palms to look at a jade amulet.

He flashes back again. He and Bai Wu Xia kneel and bow before the shrine of the fallen previous Abbot, to whom they have offered many baskets of fruit and other foods. Jue Yuan speaks aloud to the Abbot of how he is determined to enter Buddha. Bai Wu Xia gazes at him with tears in her eyes, knowing what this means. Jue Yuan vows to defend Shaolin and uphold justice, quoting the last words of his fallen Sifu, Bai Wu Xia’s father. Bai Wu Xia gives him the jade amulet, a token of her love, and departs.

Now, in the present, he looks up from the jade amulet to see Bai Wu Xia, who has sneaked into the side wing of the sanctum and is staring at him from behind a great pillar. He hesitates, then vows to remain celibate, and she leaves.

The great bell of Shaolin tolls, and the gongs and drums are beaten as Jue Yuan is ordained as a true monk of Shaolin.

The film’s closing scene is of Jue Yuan, now the new kung fu Sifu of the Shaolin Temple, leading the monks in their training.